#78 WIP: show user correct coordinates

josiahseaman · Feb 4, 2019 · fca1918 · fca1918
1 parent b183324
commit fca1918
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Showing 4 changed files with 16 additions and 17 deletions.
diff --git a/DDV/Display_Utils.ipynb b/DDV/Display_Utils.ipynb
@@ -163,7 +163,9 @@
     "collapsed": true
    },
    "outputs": [],
-   "source": []
+   "source": [
+    ""
+   ]
   },
   {
    "cell_type": "code",
@@ -512,7 +514,7 @@
     "    if score < 7000:\n",
     "        print(offset, score/len(human_sample))\n",
     "    scores.append(score/len(human_sample))\n",
-    "Pic(scores, width=len(scores), height=20)\n"
+    "Pic(scores, width=len(scores), height=20)"
    ]
   },
   {
@@ -690,7 +692,7 @@
   "language_info": {
    "codemirror_mode": {
     "name": "ipython",
-    "version": 3
+    "version": 3.0
    },
    "file_extension": ".py",
    "mimetype": "text/x-python",
@@ -765,7 +767,7 @@
     "4c67f75fbb934cca90210ad5e385736d": {
      "views": [
       {
-       "cell_index": 12
+       "cell_index": 12.0
       }
      ]
     },
@@ -799,7 +801,7 @@
     "6e9bd00ff5d64c62afe3b00f5687ee70": {
      "views": [
       {
-       "cell_index": 6
+       "cell_index": 6.0
       }
      ]
     },
@@ -917,7 +919,7 @@
     "d1fc09278f8148b9bbe6e508141868cb": {
      "views": [
       {
-       "cell_index": 14
+       "cell_index": 14.0
       }
      ]
     },
@@ -960,4 +962,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}
diff --git a/DDV/MultipleAlignmentLayout.py b/DDV/MultipleAlignmentLayout.py
@@ -136,11 +136,10 @@ def calc_all_padding(self):
             #First contig of each MSA has a 10px tall title
             contig.title_padding = 0 if i != 0 else widest_sequence * self.title_height_px
             contig.tail_padding = 0
-            contig.nuc_title_start = seq_start
-            contig.nuc_seq_start = seq_start + title_length
+            contig.nuc_seq_start = 0
             #at the moment these values are the same but they have different meanings
             total_progress += length + contig.title_padding # pointer in image
-            seq_start += title_length + length  # pointer in text
+            seq_start += length  # pointer in text
         return total_progress
 
 

diff --git a/DDV/TileLayout.py b/DDV/TileLayout.py
@@ -288,11 +288,10 @@ def calc_all_padding(self):
             contig.reset_padding = reset
             contig.title_padding = title
             contig.tail_padding = tail
-            contig.nuc_title_start = seq_start
-            contig.nuc_seq_start = seq_start + title_length
+            contig.nuc_seq_start = 0
 
             total_progress += reset + title + tail + length  # pointer in image
-            seq_start += title_length + length  # pointer in text
+            seq_start +=  length  # pointer in text
         return total_progress  # + reset + title + tail + length
 
 
@@ -548,7 +547,7 @@ def contig_struct(self):
                 {"name": contig.name.replace("'", ""), "xy_seq_start": xy_seq_start, "xy_seq_end": xy_seq_end,
                  "title_padding": contig.title_padding, "tail_padding": contig.tail_padding,
                  "xy_title_start": xy_seq_start - contig.title_padding,
-                 "nuc_title_start": contig.nuc_title_start, "nuc_seq_start": contig.nuc_seq_start,
+                 "nuc_seq_start": contig.nuc_seq_start,
                  "fake_start": fake_start})
             xy_seq_start += len(contig.seq) + contig.tail_padding
         return json
@@ -617,11 +616,10 @@ def dice_self_contigs(self, chunk_size):
 class ContigChunk(Contig):
     def __init__(self, original, fake_start, size):
         super(ContigChunk, self).__init__(original.name, original.seq[fake_start: fake_start+size])
-        self.fake_start=fake_start
+        self.fake_start = fake_start
         at_the_end = len(self.seq) != size
         first_chunk = not fake_start
         self.title_padding = original.title_padding if first_chunk else 0
-        self.nuc_title_start = original.nuc_title_start if first_chunk else fake_start
         self.nuc_seq_start = original.nuc_seq_start + fake_start
         self.tail_padding = original.tail_padding if at_the_end else 0
         self.reset_padding = original.reset_padding if at_the_end else 0

diff --git a/DDV/html_template/nucleotideNumber.js b/DDV/html_template/nucleotideNumber.js
@@ -226,7 +226,7 @@ function showNucleotideNumber(event, viewer) {
     if(cursor_in_a_title){
         document.getElementById("Nucleotide").innerHTML = position_info.contig_name;
     }else{
-        var display_number = information_to_show ? position_info.index_inside_contig : "-";
+        var display_number = information_to_show ? position_info.file_coordinates : "-";
         document.getElementById("Nucleotide").innerHTML = numberWithCommas(display_number);
         var display_file = information_to_show ? fasta_sources[position_info.fasta_index] : "Sequence under Cursor";
         document.getElementById("FileUnderCursor").innerHTML = display_file;